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新论文 · v1arXiv:2611.02506

更新于 2026-11-02

CellPlex: Benchmarking Single-Cell Spatial Proteomics Prediction from H&E

Zijun Gao, Yijiang Chen, Xiangde Luo, Pheng-Ann Heng

原文摘要

Spatial proteomics measures tens of proteins in every cell of a tissue section, but its cost confines it to small research cohorts, whereas hematoxylin and eosin (H\&E) slides exist for nearly every patient. Inferring single-cell spatial proteomics from H\&E would bring its analyses to routine pathology, and a growing number of virtual staining models pursue this goal. Each is evaluated on its own cohort, panel and pixel-level metric, and released models transfer poorly to new cohorts, leaving open which approach to build on and which proteins H\&E can reveal. We introduce CellPlex, a benchmark that poses the task at the level of the cell: seven cohorts with same-section H\&E and multiplexed immunofluorescence, from colorectal and breast cancer to lymph-node metastases, bone marrow and glioma, with 717 samples, 44.8 million cells and 149 proteins, processed by one pipeline into per-cell targets. Pathology foundation models (PFMs) are adapted with one cell-level protocol, specialist models are fine-tuned under a matched budget, and all are scored on the same cells. Adapted PFMs are the most accurate models on every cohort, ahead of the specialists even after fine-tuning, but keep less than half of their accuracy on cohorts they were not trained on. Which proteins can be predicted depends on the tissue, not on how many cells were measured for them. By fixing the cells, targets and splits on which predictions are judged, CellPlex sets a common standard for inferring costly molecular measurements from routine H\&E and shows how far H\&E can stand in for spatial proteomics. We will release the data, splits, evaluation code and baselines as a testbed for developing and comparing future pathology foundation models and virtual staining methods.

cs.CV

新论文 · v1arXiv:2610.35616

更新于 2026-10-26

Hierarchical Skill Evolution for Coding Agent

Jun Gao, Yun Peng, Changhai Zhou, Yuhan Zhu, Xiangyu Zeng, Shiyang Zhang Yuhua Zhou, Luozheng Qin, Qian Qiao 等 13 位作者

原文摘要

Skills provide agents with reusable experience to guide future decisions without modifying the underlying model. However, coding trajectories are often entangled with task- and repository-specific contexts, making it challenging to distill procedural skills that generalize across diverse coding environments. To address this challenge, we present Hierarchical Skill Evolution (HSE), which progressively distills procedural knowledge from coding trajectories through hierarchical evidence aggregation. HSE first extracts task-level evidence from individual trajectories, then aggregates recurring evidence within the same repository to form repository-specific skill candidates, and finally consolidates consistent patterns across repositories into transferable skills across repositories. The evolution is driven by an external writer-evaluator loop that generates and assesses skills while keeping the underlying coding model frozen. The loop externally updates the writer and evaluator policies to improve subsequent skill generation and assessment. This hierarchy progressively filters task-specific details while preserving procedures that generalize across diverse coding environments. Successful trajectories yield reusable guidance for future tasks, while failed trajectories reveal recurring failure modes that guide avoidance and recovery. We evaluate HSE on SWE-bench Verified and DeepSWE, using GLM-5.2 across Pi and Claude Code harnesses and GPT-5.5 and Opus 4.8 with Pi. Across both benchmarks, 10 skills evolved solely from SWE-Gym improve coding performance across all evaluated settings, demonstrating transfer across benchmarks, coding models, and agent harnesses. We further evolve the skill library from target-benchmark trajectories without verifier feedback, relying solely on the learned evaluator for candidate assessment and achieving additional gains through benchmark-tailored skills.

cs.CL

版本更新 · v2arXiv:2610.22276

更新于 2026-10-26

MJev-Spatial: System One Spatial Intelligence via Native Attention Matching

Luozheng Qin, Yuhan Zhu, Changhai Zhou, Qian Qiao, Jun Gao, Yuhua Zhou, Harry Zhang, Xiangyu Zeng 等 13 位作者

原文摘要

Spatial intelligence lets an agent perceive and act in the physical world, and many of its judgments must be made at interaction rates: which spatial relation holds, how far an object is, or where to place it. Vision-language models (VLMs) produce these answers by free-form text generation, paying for autoregressive decoding and answer parsing even though the output space is compact: one of a few options, a scalar, or a 2D point. In light of this, we introduce MJev-Spatial, a System 1 multimodal decision model that tackles all three types of spatial understanding tasks within a unified classification framework. Specifically, MJev-Spatial treats each candidate as a class and scores it using the backbone's pretrained query and key projections, without adding parameters. The candidates are the given options for choice tasks, or value bins and image regions refined through coarse-to-fine classification for numerical and point prediction, respectively. At inference, each classification decision takes a single forward pass and generates no answer tokens. To train on heterogeneous spatial data efficiently, we supervise all coarse-to-fine stages jointly with teacher forcing in one forward pass, and combine this with length-aware global batching and cross-GPU load balancing, raising training throughput by 30.8% over the original batching strategy. Built on Qwen3.5-4B and trained on 12.3M question-answer pairs converted from existing spatial datasets, MJev-Spatial achieves the highest overall score (65.64%) among eight tested models, ranks first on seven of twelve benchmarks, and outperforms its unmodified autoregressive base model on all twelve, while running 2.5 times faster than the fastest autoregressive baseline and 5.6 times faster than the base model.

cs.CV

版本更新 · v2arXiv:2608.27549

更新于 2026-10-26

Code as Worlds: Agentic Discovery of Executable World Representations for Physical Reasoning

Hanyang Wang, Yimo Cai, Weiliang Chen, Jiawei Chi, Haowen Sun, Qiyu Dai, Yi-Hsin Hung, Xingzhuo Guo 等 17 位作者

原文摘要

Physical understanding and reasoning depend on forming compact and generalizable representations of the world. While modern vision-language models can recognize and explain diverse physical events, they often lack explicit representations of the underlying mechanisms-such as object states, physical parameters, and governing dynamics-needed for reliably reasoning how the world evolves and responds to interventions. In this work, we introduce Code-as-World, a paradigm that represents physical worlds through executable world representations. By expressing physical composition, dynamic evolution, and visual appearance as executable code, Code-as-World provides a compact, quantitatively grounded, and controllable abstraction of the physical world. To construct such representations from multimodal observations, such as natural-language descriptions or real-world videos, we develop an agentic discovery loop inspired by abductive reasoning, where an agent proposes, executes, renders, verifies, and iteratively refines executable world hypotheses. As a concrete application, we use verified executable worlds to provide scalable physical supervision for training vision-language models on quantitative physical reasoning. Experiments show that Code-as-World-VL achieves state-of-the-art performance on QuantiPhy and surpasses leading proprietary models, highlighting the potential of executable world representations as a scalable foundation for physical intelligence.

cs.CV

版本更新 · v2arXiv:2606.02552

更新于 2026-10-26

Modeling Depth Ambiguity: A Mixture-Density Representation for Flying-Point-Free Depth Estimation

Siyuan Bian, Congrong Xu, Jun Gao

原文摘要

Despite advances in depth estimation, flying points remain a persistent failure mode: near object boundaries, depth estimators often predict spurious 3D points in the empty space between foreground and background surfaces. We trace this artifact to a standard modeling choice: assigning each pixel a single depth hypothesis. At boundaries, a pixel can straddle a foreground and a background surface, so its true depth is ambiguous between the two. A model that predicts a single depth cannot keep both possibilities, so training instead pulls the prediction toward an intermediate depth that lies on neither surface. We address this with MDA, a mixture-density representation that lets the model predict multiple depth hypotheses and their associated probabilities for each pixel. Near boundaries, different hypotheses can align with different surfaces, and the decoded depth is selected from one of these hypotheses rather than placed in the empty space between them. Across different architectures, MDA substantially improves boundary reconstruction over each base model and largely removes flying-point artifacts even under severe input blur, while adding negligible runtime overhead. The same mixture-density framework naturally extends to transparent objects, where it predicts multiple depth layers at transparent pixels, and to sky regions, where a dedicated component separates the unbounded sky from finite-depth regions, producing flying-point-free skylines.

cs.CV · cs.AI

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.1783ACL Anthology · ACL 2026

来源日期 2026-07-01（仅到月份）

HumanLLM: Benchmarking and Improving LLM Anthropomorphism via Human Cognitive Patterns

Xintao Wang, Jian Yang, Weiyuan Li, Rui Xie Fudan University, Jen-tse Huang, Jun Gao Momo Inc., Shuai Huang, Yueping Kang hellogroup 等 11 位作者

原文摘要

Large Language Models (LLMs) have demonstrated remarkable capabilities in reasoning and generation, serving as the foundation for advanced persona simulation and Role-Playing Language Agents (RPLAs). However, achieving authentic alignment with human cognitive and behavioral patterns remains a critical challenge for these agents. We present HumanLLM, a framework treating psychological patterns as interacting causal forces.We construct 244 patterns from \sim12,000 academic papers and synthesize 11,359 scenarios where 2-5 patterns reinforce, conflict, or modulate each other, with multi-turn conversations expressing inner thoughts, actions, and dialogue.Our dual-level checklists evaluate both individual pattern fidelity and emergent multi-pattern dynamics, achieving strong human alignment (r=0.90) while revealing that holistic metrics conflate simulation accuracy with social desirability.HumanLLM-8B outperforms Qwen3-32B on multi-pattern dynamics despite 4\times fewer parameters, demonstrating that authentic anthropomorphism requires cognitive modeling—simulating not just what humans do, but the psychological processes generating those behaviors.Our dataset, code, and model are available at:https://github.com/YJGoodbye2024/HumanLLM

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.182ACL Anthology · ACL 2026

来源日期 2026-07-01（仅到月份）

Can We Predict Before Executing Machine Learning Agents?

Jingsheng Zheng, Jintian Zhang, Yujie Luo, Yuren Mao, Yunjun Gao Zhejiang University, Lun Du Ant Group, Huajun Chen Zhejiang University and ZJU-Hangzhou Global Scientific and Technological Innovation Center, Ningyu Zhang Zhejiang University

原文摘要

Autonomous machine learning agents have revolutionized scientific discovery, yet they remain constrained by a Generate-Execute-Feedback paradigm. Previous approaches suffers from a severe Execution Bottleneck, as hypothesis evaluation relies strictly on expensive physical execution. To bypass these physical constraints, we internalize execution priors to substitute costly runtime checks with instantaneous predictive reasoning, drawing inspiration from World Models. In this work, we formalize the task of Data-centric Solution Preference and construct a comprehensive corpus of 18,438 pairwise comparisons. We demonstrate that LLMs exhibit significant predictive capabilities when primed with a Verified Data Analysis Report, achieving 61.5% accuracy and robust confidence calibration. Finally, we instantiate this framework in ForeAgent, an agent that employs a Predict-then-Verify loop, achieving a 6x acceleration in convergence while surpassing execution-based baselines by +6%.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.1966ACL Anthology · ACL 2026

来源日期 2026-07-01（仅到月份）

LogosKG: Hardware-Optimized Scalable and Interpretable Knowledge Graph Retrieval

He Cheng, Yifu Wu AWS, Saksham Khatwani, Maya Kruse University of Colorado Anschutz Medical Campus, Dmitriy Dligach Loyola University Chicago, Timothy A. Miller, Majid Afshar University of Wisconsin - Madison, Yanjun Gao University of Colorado Anschutz Medical Campus

原文摘要

Knowledge graphs (KGs) are increasingly integrated with large language models (LLMs) to provide structured, verifiable reasoning. A core operation in this integration is multi-hop retrieval, yet existing systems struggle to balance efficiency, scalability, and interpretability. We introduce LogosKG, a novel, hardware-aligned framework that enables scalable and interpretable k-hop retrieval on large KGs by building on symbolic KG formulations and executing traversal as hardware-efficient operations over decomposed subject, object, and relation representations. To scale to billion-edge graphs, LogosKG integrates degree-aware partitioning, cross-graph routing, and on-demand caching. Experiments show substantial efficiency gains over CPU and GPU baselines without loss of retrieval fidelity. With proven performance in KG retrieval, a downstream two-round KG-LLM interaction demonstrates how LogosKG enables large-scale, evidence-grounded analysis of how KG topology, such as hop distribution and connectivity, shapes the alignment between structured biomedical knowledge and LLM diagnostic reasoning, thereby opening the door for next-generation KG-LLM integration. The source code is publicly available at https://github.com/LARK-NLP-Lab/LogosKG, and an online demo is available at https://lark-nlp-lab-logoskg.hf.space/.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.572ACL Anthology · ACL 2026

来源日期 2026-07-01（仅到月份）

The Bidirectional Process Reward Model

Lingyin Zhang, Jun Gao, Xiaoxue Ren Zhejiang University, Ziqiang Cao Soochow University, China

原文摘要

Process Reward Models (PRMs), which assign fine-grained scores to intermediate reasoning steps within a solution trajectory, have emerged as a promising approach to enhance the reasoning quality of Large Language Models (LLMs).However, most existing PRMs rely on a unidirectional left-to-right (L2R) evaluation scheme, which restricts their utilization of global context.In light of this challenge, we propose a novel bidirectional evaluation paradigm, named \mathbf{Bi}directional \mathbf{P}rocess \mathbf{R}eward \mathbf{M}odel (\mathbf{BiPRM}).BiPRM incorporates a parallel right-to-left (R2L) evaluation stream, implemented via prompt reversal, alongside the conventional L2R flow.Then a gating mechanism is introduced to adaptively fuse the reward scores from both streams to yield a holistic quality assessment.Remarkably, compared to the original PRM, BiPRM introduces only a 0.3% parameter increase for the gating module, and the parallel execution of two streams incurs merely 5% inference time latency. Our extensive empirical evaluations spanning diverse benchmarks, LLM backbones, PRM objectives and sampling policies demonstrate that BiPRM consistently surpasses unidirectional baselines, achieving an average relative gain of 10.6% over 54 solution-level configurations and 37.7% in 12 step-level error detection scenarios.Generally, our results highlight the effectiveness, robustness and general applicability of BiPRM, offering a promising new direction for process-based reward modeling.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表